Beagle(1) Genotype calling, genotype phasing and imputation of ungenotyped markers


java -Xmx[GB]g -jar /usr/share/beagle/beagle.jar [options]


Beagle performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. Genotypic imputation works on phased haplotypes using a Li and Stephens haplotype frequency model. Beagle also implements the Refined IBD algorithm for detecting homozygosity-by-descent (HBD) and identity-by-descent (IBD) segments.


Data input/output parameters

Specifies a VCF file containing a GT (genotype) format field for each marker. If a genotype contains the phased allele separator, "|", then Beagle will preserve the phase of the genotype during the analysis. If you use the gt argument, all genotypes in the output file will be phased and non-missing.
Specifies a VCF file containing a GL or PL (genotype likelihood) format field for each marker. Any data in the GT format field will be ignored. If both GL and PL format fields are present for a marker, the GL format will be used.
Specifies a VCF file containing a GT, GL or PL format field for each marker. If a genotype is non-missing, Beagle will ignore the genotype likelihood. If both GL and PL format fields are present for a marker, the GL field will be used.
Specifies a VCF file containing phased reference genotypes. See the impute parameter.
Specifies the output filename prefix. The prefix may be an absolute or relative filename, but it cannot be a directory name.
Specifies a file containing non-reference samples (one sample per line) to be excluded from the analysis and output files.
Specifies a file containing markers (one marker per line) to be excluded from the analysis and the output files. An excluded marker identifier can either be an identifier from the VCF record’s ID field or a genomic coordinate in the format: CHROM:POS.
Specifies a PLINK format genetic map on the cM scale. HapMap GrCh36 and GrCh37 genetic maps in PLINK format are available for download from the Beagle website. Use of a genetic map is recommended if you are imputing ungenotyped markers. If no genetic map is specified, Beagle will assume a constant recombination rate of 1 cM / Mb.
Specifies a chromosome or chromosome interval using a chromosome identifier in the VCF file and the starting and ending positions of the interval. The entire chromosome, the beginning of the chromosome, and the end of a chromosome can be specified by chrom=[chrom], chrom=[chrom:-end], and chrom=[chrom:start-] respectively.
Default = 5000
Specifies the maximum likelihood ratio at a genotype. If M is the maximum of the likelihoods of each possible genotype, any likelihood that is less than (M ⁄ maxlr) is set to 0.0 to improve computational efficiency.

General parameters

Default: machine-dependent
Specifies the number of threads of execution. If no nthreads parameter is specified, the nthreads parameter will be set equal to the number of CPU cores on the host machine.
Default = false
Specifies whether a memory efficient algorithm should be used. The memory efficient algorithm increases run-time by a factor less than 2.0.
Default = 50000
Specifies the number of markers to include in each sliding window. The window parameter must be at least twice as large as the overlap parameter. The window parameter controls the amount of memory used in the analysis. For human data, it is recommended that the window parameter be greater than or equal to the typical number of markers in 5 cM.
Default = 3000
Specifies the number of markers of overlap between sliding windows. For human data, it is recommended that the overlap be set to the typical number of markers in 0.5 cM (when ibd=false) or 2.0 cM (when ibd=true).
Default = -99999
Specifies the seed for the random number generator.

Phasing and imputation parameters

Default = 5
Specifies the number of phasing iterations. The phasing iterations are preceded by 10 burn-in iterations which carry out the Beagle version 4.0 phasing algorithm. If you want to phase your data with the Beagle 4.0 phasing algorithm, use niterations=0. Accuracy and compute time increase with the number of iterations.
Default = true
Specifies whether markers that are present in the reference panel but absent in your data will be imputed. This option has no effect if the ref and gt arguments are not used.
Default = false
Specifies whether a GP (genotype probability) format field will be included in the output VCF file when imputing ungenotyped markers. By default, a GP fields is not printed because a DS (alternate allele dose) format field is always printed when imputing ungenotyped markers.
Default = 1000000
Specifies the effective population size when imputing ungenotyped markers. The default value is suitable for a large outbred human population. Smaller values in the hundreds or thousands for the ne parameter are suggested for inbred human and animal populations.
Default = 0.0001
Specifies the allele miscall rate. The default value should give good results for most sequence and SNP array data.
Default = 0.005
Specifies the maximum cM distance between individual markers that are combined into an aggregate marker when imputing ungenotyped markers.

IBD parameters

Default = false
Specifies whether IBD analysis will be performed when the gt argument is used.
Default = 3.0
Specifies the minimum LOD score for reported IBD.
Default: data-dependent
Specifies the scale parameter used to build the haplotype frequency model for IBD analysis. If no ibdscale parameter is specified the scale parameter for the IBD analysis will be set to max{2, sqrt[sample size]/100}, which we have found to work well for outbred populations.
Default = 40
Specifies the number of markers trimmed from the end of a shared haplotype when testing for IBD. Note: The default ibdtrim parameter is designed for European samples genotyped with a 1M SNP array (~ 1 marker per 3 kb). For human SNP array data, it is recommended to set the ibdtrim parameter to the typical number of markers in a 0.15 cM region. Pilot studies of randomly selected genomic regions can be used to fine-tune the values of the ibdtrim parameter.


Beagle was written by Brian L. Browning.

This manual page was written by Dylan Aïssi <[email protected]>, for the Debian project (but may be used by others).